Centre for Arthritis Diagnostic and Therapeutic Innovation - Core Facilities

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Next Generation Sequencing Core Facility

 

The Centre for Arthritis Diagnostic and Therapeutic Innovation brings cost-effective Next-Generation Sequencing solutions to the Krembil Brain Institute. We aim to foster collaboration and to help advance the research of Krembil Investigators working in the fields of arthritis, brain and vision.

 

Our sequencing team consists of our sequencing specialist, Keemo Delos Santos, who oversees the operations of the facility, coordinates the projects, assesses quality control of samples and sequencing library preparation, and conducts any necessary training and troubleshooting on library preparation; Pratibha Potla, our bioinformatician conducts the initial analysis and sequence alignment. Dr. Osvaldo Espin-Garcia is our senior biostatistician who mines the data and performs the statistical analyses; Dr. Shabana Vohra is our senior bioinformatician with specific expertise in single-cell RNA sequencing, single-nucleus RNA sequencing and spatial transcriptomics; and Dr. Chiara Pastrello, our computational biologist who identifies signalling pathways and networks related to the potential differentially expressed targets emerging from the sequencing experiments.

Sequencing Team

Sequencing Team, from left to right, Dr. Starlee Lively, Pratibha Potla, Dr. Osvalodo Espin-Garcia, Dr. Anusha Ratenswaren  

For quotes and initial consultation, please contact Keemo Delos Santos.

This Centre is directed by Dr. Mohit Kapoor​

Metabolomics Core Facility

As an emerging field in systems biology and a new branch in the field of "omics", metabolomics – which is the study of all the small molecules (<1500 Da) within a system – is gaining much interest in the scientific community, particularly in clinical research. Due to the close and near-instantaneous relationship of the metabolome with a biological state (healthy vs. disease), metabolites generally present as rapid indicators of perturbances within a dynamic biological system. As such, metabolomics can be used as a tool in clinical research for determining disease pathology, thereby helping to pave an alternative path towards improved engineering of treatments of various diseases.

At the Schroeder Arthritis Institute's Centre for Diagnostic and Therapeutic Innovation – Metabolomics Core Facility, liquid chromatography coupled to high-resolution mass spectrometry (LC-HRMS) is the platform of choice for conducting metabolomics studies. Our LC-HRMS equipment – a Thermo Scientific™ Vanquish™ Flex Binary UHPLC system utilized in combination with a Thermo Scientific™ Q Exactive™ Plus Hybrid Quadrupole-Orbitrap™ mass spectrometer (MS) – is dedicated to the evaluation and elucidation of metabolites from biological cells, tissues and fluids. This metabolomics platform provides high accuracy, precision and reproducibility via the high-throughput capabilities of the robust and reliable UHPLC system that can perform superior separation of metabolites originating from complex biological sources. In addition, the MS boasts technology for optimal precursor ion selection, molecular fragmentation, and is equipped with an Orbitrap™ mass analyzer with a resolution of up to 140 000, making it the ideal instrumentation for the identification and analysis of known and/or unknown small molecules.

The Metabolomics Workflow

To apply metabolomics to your research, whether hypothesis- (targeted) or non-hypothesis- (untargeted/discovery) driven, the steps of the metabolomics workflow are as outlined below. Since metabolomics studies start with the biological question, please email it to Nikita Looby to get started!

A general price list that is associated with sample preparation and the use of the LC-HRMS system can be found below. A more accurate quote that is specific to your research needs can be generated by filling out the Request for Quotation.

This core facility is currently being developed under the supervision of Dr. Vinod Chandran and Dr. Mohit Kapoor.


Metabolomics workflow  

Schroeder Arthritis Metabolomics Core Facility Price List

Sample Preparation using SPME

Item Cost (CAD)
Biological fluids (i.e., plasma, serum, urine, CSF etc.) (≥100µL) $65 - $85 per sample

LC- HRMS Analysis

Item Academia Cost (CAD) Industry Cost (CAD)
Untargeted metabolomics
Base rate
$400 $800
Cost per sample OR per hour for multiple samples *
General metabolomics (RPLC) $85 - $120 $170 - $240
Lipidomics (RPLC) $105 - $145 $210 - $290
Polar metabolites (HILIC) $125 - $175 $250 - $350
* LC columns + column accessories can be purchased independently. A discount of $10 per sample OR per hour will apply in these cases.
Interest in ESI (+) and ESI (-) mode runs qualify for a double mode discount.

Sample Requirements

  • A minimum of 48 independent samples is required. For ≤48 samples, a premium will apply.
  • Projects with many samples qualify for high-volume discounts.
  • For projects with a large sample size, a preliminary run on a subset of samples is recommended and can be arranged.

Statistical Analysis

TBD


Prices are valid from January 1, 2022 to December 1, 2022 and are subject to annual readjustment.


Informatics Core Facility

The Informatics core brings cost-effective integrative computational biology solutions to the Schroeder Arthritis Institute. We aim to foster collaboration and to help advance the research of Schroeder Investigators working across spectrum of arthritis conditions. The Informatics core is directed by Dr. Igor Jurisica

Available analysis pipeline
Arrow progression left to right of analysis  

The collaborative process begins by consulting with the Computational Biologist to plan, design and budget for the analyses of interest. Our Computational Biologist will work closely with lab personnel to identify the analyses more appropriate to answer the research questions at hand and will be providing updates at specific checkpoints. After completion of the analyses, details about methods and resources used as well as results in table and publication-ready image format will be provided to the lab contact person.

For quotes and initial consultation, please contact our Computational Biologist, Dr. Chiara Pastrello.​

Biobank Core Facility

 

The Schroeder Arthritis Institute Biobank is one of the largest biobanks with over 500,000 high-quality samples. This biobank is comprised of biospecimens collected from our clinics, national and international collaborators and represents various forms of arthritis:

  1. Orthopaedics and Osteoarthritis (OA) Biobank:
    Cohorts include: end-stage OA knee, hip OA, spine OA, ankle OA, shoulder OA, elbow OA and hand OA; early OA knee; post-traumatic knee OA; normal cartilage spine patients; conservative hand patients and a healthy control group from volunteers.
    Samples include longitudinal biofluids such as plasma, urine and whole blood, as well as surgical tissues and synovial fluid.
  2. Rheumatology Biobank
    Cohorts include: psoriatic arthritis (PsA); psoriasis (Ps); ankylosing spondylitis (AS); Systemic Lupus Erythematosus (SLE) and healthy controls.
    Samples include derivatives from bio-fluids such as blood, synovial fluid, urine, semen and stool as well as tissue biopsies.

All biospecimens are located in a key-card access, remote temperature monitored location until further analysis is requested. The sample request undergoes ethical monitoring and governance to ensure compliance with all policies and guidelines from the Research Ethics Board and principal investigators are met.

If you are interested in more details about this biobank, please contact our biobank operations co-chairs Kim Perry and Julie Gagnier.​​